Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_011814326.1 HHAL_RS07765 UDP-glucose 4-epimerase GalE
Query= SwissProt::P24325 (338 letters) >NCBI__GCF_000015585.1:WP_011814326.1 Length = 339 Score = 396 bits (1018), Expect = e-115 Identities = 190/330 (57%), Positives = 242/330 (73%) Query: 1 MAILVTGGAGYIGSHTVVELLNVGKEVVVLDNLCNSSPKSLERVKQITGKEAKFYEGDIL 60 M +LVTGG GYIGSH V L+ G E V+LDN NS+ R+ +IT + GD+ Sbjct: 1 MRVLVTGGTGYIGSHAAVALIEAGHEAVLLDNQHNSTGAVASRIGRITRTSPELIRGDVR 60 Query: 61 DRALLQKIFAENEINSVIHFAGLKAVGESVQKPTEYYMNNVAGTLVLIQEMKKAGVWNFV 120 D ++L ++F+ I++V+HFAGLKAVGESVQ+P +YY NV GT+ L Q M+ AGV + Sbjct: 61 DASMLAELFSARRIDAVMHFAGLKAVGESVQRPLDYYETNVGGTIRLCQAMEAAGVRKLI 120 Query: 121 FSSSATVYGDPKIIPITEDCEVGGTTNPYGTSKYMVEQILRDTAKAEPKFSMTILRYFNP 180 FSSSATVYGDP +PI ED GGTTNPYGTSK+MVE++L D + A P + + ILRYFNP Sbjct: 121 FSSSATVYGDPDRVPIREDAPTGGTTNPYGTSKHMVERMLTDLSTANPGWCIGILRYFNP 180 Query: 181 VGAHESGLIGEDPNGIPNNLLPYISQVAIGKLAQLSVFGSDYDTHDGTGVRDYIHVVDLA 240 VGAH+S LIGE P+GIPNNL+PYI+QVA G+ L VFG DY T DGTGVRDYIHVVDLA Sbjct: 181 VGAHKSALIGESPSGIPNNLVPYIAQVAAGEREHLQVFGDDYPTRDGTGVRDYIHVVDLA 240 Query: 241 VGHLKALQRHENDAGLHIYNLGTGHGYSVLDMVKAFEKANNITIAYKLVERRSGDIATCY 300 GH++AL+ + G H +NLG G G+SVL+ V+AFE+A+ +I Y++ ERR GD+A C+ Sbjct: 241 AGHVRALEYLDAQPGQHAWNLGRGEGHSVLEAVRAFEQASGCSIPYRVTERRPGDVAECW 300 Query: 301 SDPSLAAKELGWVAERGLEKMMQDTWNWQK 330 +DPS A +ELGW AERGL MM+D W WQ+ Sbjct: 301 ADPSKAERELGWRAERGLATMMEDAWRWQR 330 Lambda K H 0.316 0.135 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 404 Number of extensions: 10 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_011814326.1 HHAL_RS07765 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01179.hmm # target sequence database: /tmp/gapView.2580.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01179 [M=332] Accession: TIGR01179 Description: galE: UDP-glucose 4-epimerase GalE Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-137 443.8 0.0 1.7e-137 443.7 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011814326.1 HHAL_RS07765 UDP-glucose 4-epime Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011814326.1 HHAL_RS07765 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.7 0.0 1.7e-137 1.7e-137 1 328 [. 2 332 .. 2 336 .. 0.98 Alignments for each domain: == domain 1 score: 443.7 bits; conditional E-value: 1.7e-137 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 ++LvtGg+GyiGsh +++l e+g+e v+lDn +++ + +++ +it + +l++gd++d+++l+++++ lcl|NCBI__GCF_000015585.1:WP_011814326.1 2 RVLVTGGTGYIGSHAAVALIEAGHEAVLLDNQHNSTGAVASRIGRITrtSPELIRGDVRDASMLAELFS 70 69***********************************999999999977889***************** PP TIGR01179 68 eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEe 136 +++idav+Hfa+l+avgEsv++Pl YYe nv +t++L++am++agv+kliFsssa+vYg++++vpi E+ lcl|NCBI__GCF_000015585.1:WP_011814326.1 71 ARRIDAVMHFAGLKAVGESVQRPLDYYETNVGGTIRLCQAMEAAGVRKLIFSSSATVYGDPDRVPIRED 139 ********************************************************************* PP TIGR01179 137 spln.pinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaeva 203 +p++ ++npYG+sk mvEr+l+dl++a++++ + iLRYFn++GA+++ iGe++++++ +l++++a+va lcl|NCBI__GCF_000015585.1:WP_011814326.1 140 APTGgTTNPYGTSKHMVERMLTDLSTANPGWCIGILRYFNPVGAHKSALIGESPSGIPnNLVPYIAQVA 208 ***99*****************************************************9********** PP TIGR01179 204 vgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavk 272 +g+re+l++fG+dypt+DGt+vRDyiHv Dla++H++ale+l ++ +++++nlG g+g+sv+e ++a++ lcl|NCBI__GCF_000015585.1:WP_011814326.1 209 AGEREHLQVFGDDYPTRDGTGVRDYIHVVDLAAGHVRALEYLDAQPGQHAWNLGRGEGHSVLEAVRAFE 277 ********************************************************************* PP TIGR01179 273 kvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 ++sg +i++++++rR+GD+a+++ad+sk++relgw+++++ L++++++aw+W+++ lcl|NCBI__GCF_000015585.1:WP_011814326.1 278 QASGCSIPYRVTERRPGDVAECWADPSKAERELGWRAERG-LATMMEDAWRWQRQG 332 ****************************************.************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (339 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.13 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory